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Abiogenesis Challenge

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Over on a recent thread, we witnessed some flailing about with respect to abiogenesis (see comments 374-376). Thoroughly confused about critical distinctions, such as the difference between deterministic forces and contingent possibilities, some seem to think that the fact that “nature forms stars and planets” means that nature can do just about anything. No need to ask any hard questions, kids! Just close your eyes and imagine the possibilities.

This is what so much of the materialistic abiogenesis creation story amounts to.

I have posted essentially this challenge before, but for Zachriel and anyone else who thinks materialistic abiogenesis is anything more than a laughable made-up story, here it is again:

—–

For purposes of this challenge, I’m willing to grant you all the amino acids you want. I’ll even give them all to you in a non-racemic mixture. You want them all left-handed? No problem. I’ll also grant you the exact relative mixture of the specific amino acids you want (what percentage do you want of glycine, alanine, arginine, etc.?). I’ll further give you just the right concentration to encourage optimum reaction. I’m also willing to give you the most benign and hospitable environment you can possibly imagine for your fledgling structures to form (take your pick of the popular ideas: volcanic vents, hydrothermal pools, mud globules, tide pools, deep sea hydrothermal vents, comets, dust clouds in space . . . whichever environment you want). I’ll even throw in whatever type of energy source you want in true Goldilocks fashion: just the right amount to facilitate the chemical reactions; not too much to destroy the nascent formations. I’ll further spot you that all these critical conditions occur in the same location spatially. And at the same time temporally. Shoot, as a massive bonus I’ll even step in to prevent contaminating cross reactions. I’ll also miraculously make your fledgling chemical structures immune from their natural rate of breakdown.

Every single one of the foregoing items represents a huge challenge to the formation of life, but I’m willing to grant them all for the present exercise.

Now, with all these concessions, go ahead, what is your theory about how life formed?

—–

Note:

I also reiterate my open invitation for Zachriel, AVS, billmaz and anyone else to do a guest post laying out their strongest evidence for abiogenesis. There have been no takers yet, but the invitation remains open.

Comments
Eric Anderson: The challenge in the OP remains. Szostak's Lab provides an overview of what is known, including challenges that remain. Eric Anderson: Not “presumably meaning Shannon information.” What kind of information is being "removed" when there is selection for color in peppered moths, per Box's comment? Eric Anderson: Finally, your continued assertions about the definition of “evolution” ... Call it Fred if it makes you feel any better. But in biology, evolution generally refers to change in heritable traits in populations. Numerous citations have been provided in support of this usage. What you want to talk about is complex adaptation, which is fine, but it's very difficult to talk about scientific topics when words get redefined. You can't even make sense of scientific research papers. EugeneS: There can be no demonstration of anything relating to past. At best, it is possible to support certain hypotheses by experimentation. We can demonstrate that dinosaurs roamed the Earth. Zachriel: That’s what demonstrate means in science. EugeneS: Demonstration of validity of a theory refers to something extraneous to the theory. In the case of the great age of the Earth, that evidence includes geological data and radiometrics, both otherwise independent of the age of the Earth. We also have strong support in astronomy for how planets form. EugeneS: E.g. measuring genome homology does not demonstrate common descent but rather assumes it. Homology is determined by finding evidence of ancestry. If silent mutations in a group of genes form a nested hierarchy, then it indicates homology. EugeneS: In order to demonstrate abiogenesis, one must obtain a living cell without recourse to controlled synthesis. It requires showing it could occur in plausible primordial conditions.Zachriel
November 21, 2015
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Enzymes are protein catalysts Ribozymes are RNA catalysts End of story. Those are the correct definitions. Anything you look up that says different is either due to over-simplification, the word is being used colloquially, or they’re just flat-out wrong. When someone wants to talk about my comment @251, which is an attempt to answer EA's question (who has since disappeared), I'll be here.Alicia Cartelli
November 21, 2015
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Alicia is trolling.
Makin' Zachy jealous. Whoop! I went there! Andrewasauber
November 21, 2015
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Alicia Cartelli:
And your inability to come up with the enzyme name is equivalent to an admission that it doesn’t exist.
What part of you already admitted that it exists do you not understand? What part of you're not debating the name but the actual existence do you not understand? After denying it's existence, and rejecting the claim that you were merely arguing over how it was named, you have no honest recourse to some alternate universe in which all that did not happen. Ugly. Facts.Mung
November 20, 2015
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In case anyone wonders what Alicia is nattering on about... AC:
...there are really no “peptidyl transferase” enzymes...
They don't exist. AC:
I’m done with you; you will not be able to find an enzyme that “detaches the amino acid from the tRNA so that it can be added to the peptide chain,” other then the ribosome (which as I said from the beginning is technically a ribozyme, despite incorrect usage of the term “enzyme” even by researchers).
They do exist. Apparently it's a disagreement over naming. And around and around we go. But isn't that what trolls do? Mung:
You claimed it did not exist. You are wrong. You also said you weren’t arguing about the name, but about whether or not it existed. It exists. Even you admit that. So now you all of a sudden want to argue about it’s name.
Alicia loses. credibility shot. period. for the onlookers:
peptidyltransferase – the ribosomal enzyme that catalyzes the elongation step in polypeptide synthesis – Oxford Dictionary of Biochemistry and Molecular Biology
The crystallographic structures compellingly confirmed that peptidyl transferase is an RNA enzyme.
see also Anyways. Alicia has nothing in response to the OP, which is why she's willing to discuss anything but the OP.Mung
November 20, 2015
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Why do you think I commented here in the first place, Mungy? And your inability to come up with the enzyme name is equivalent to an admission that it doesn't exist. I'm still waiting for some kind of a response to my comment @251. Should be interesting to see what a bunch of scientifically illiterate, biologically-challenged UDiots come up with. I'll be patiently waiting!Alicia Cartelli
November 20, 2015
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Alicia Cartelli:
I’m done with you Mungy, say whatever you want, just know that it’s probably wrong.
I say that you find me irresistible. :)Mung
November 20, 2015
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Alica Cartelli: Until then, your not worth the breath. Where have I heard that before? Alicia Cartelli:
Until you come up with the enzyme or admit that it doesn’t exist, I will not be responding to you. Toodaloo!
Given that you would not be responding to me again until I came up with the name of the enzyme or admitted that it doesn't exist... And given that you have indeed responded to me... Either I came up with the name of the enzyme... Or I admitted it doesn't exist... Or... well... you figure it out.Mung
November 20, 2015
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Oh Alicia,
Everything in biology points to chemical/biological evolution producing life and eventually the diversity of species we see today. Why not informally hypothesize about what the earliest systems could have been.
Indeed. This is the thread for you, then. Or not.Mung
November 20, 2015
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Oh Mungy. When you come up with the name of an enzyme that “detaches the amino acid from the tRNA so that it can be added to the peptide chain,” that isn’t “the ribosome," then I'll respond. Until then, your not worth the breath.Alicia Cartelli
November 20, 2015
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Eric Anderson @ 240:
Alicia Cartelli: We note for the record your flippant and arrogant attitude, all the while failing to provide any evidence to support the naturalistic abiogenesis storyline.
Alicia is trolling. Check out her comment here:
Everything in biology points to chemical/biological evolution producing life and eventually the diversity of species we see today. Why not informally hypothesize about what the earliest systems could have been. I’m just here for some friendly banter, but it’s tough to do when nobody else understands molecular biology. Guess I should’ve known better.
Two birds. One stone. AC down. And I don't mean feathers.Mung
November 20, 2015
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@266 Mung laying the smack down on the troll.Jack Jones
November 20, 2015
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Of course you are Alicia. You made a fool of yourself, and now you're making your "last stand." But we know you're just here for amusement, isn't that what you said? I can go look it up for you if you like. Just another troll, in a long line of trolls. But you're special, in your own sort of weird way. 1.) you don't know what an enzyme is. 2.) you don't know that peptidyltransferase is an enzyme. 3.) But you're here to teach us all how we're a bunch of ignoramuses. You go girl!Mung
November 20, 2015
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Still waiting for you come up with the name of an enzyme that “detaches the amino acid from the tRNA so that it can be added to the peptide chain,” that isn’t “the ribosome.” Any day now mungy.Alicia Cartelli
November 20, 2015
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Alicia Cartelli:
“Right, but you can’t get that initial ribozyme without an intelligent designer.” False. Ribozyme is a strand of nucleic acid folded in on itself.
Let me see if I have this right. Any old bit of RNA that folds on itself is a ribozyme? No enzymatic activity required? You must think ribozyme is a complete misnomer. Or maybe you don't know what an enzyme is.Mung
November 20, 2015
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Shannon information is important in biological systems, not because it tells us what information is, but because it provides is with a measure. Which is why I think a better term for it is the Shannon measure of information, or SMI. So what does SMI measure? As pointed out by KF above, carrying capacity. If we are in fact speaking of the transfer of recorded information, then information theory is of obvious relevance. The trick is to find the right way to talk about it. Not to try to take the thread off-track. :)Mung
November 20, 2015
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Alicia Cartelli: You present an IF statement and then test it. Yes, we've been trying that approach with you. IF you know what an enzyme is and IF you know what peptidyltransferase is THEN you would know that peptidyltransferase is an enzyme. But you failed. credibility. shot. Alicia Cartelli: Do you know nothing about science or do you just love the word “IF?” How wonderfully ironic of you. Troll less please.Mung
November 20, 2015
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Has anyone even made an attempt yet? Reminds me of the challenge issued by KF. Naysayers by the score, but nary a brave soul in sight. Especially lacking, competent biologists.Mung
November 20, 2015
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Mr Anderson. Are you going to do a follow up post on the results of your challenge? It doesn't look good for those that believe in a living organism originating spontaneously from non living matter in a natural environment.Jack Jones
November 20, 2015
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Lizzy, the combinatorial explosion is the merciless killer of Darwinism. Abiogenesis is just chicken feather voodoo science. You lose and so do all the other math-challenged dirt worshipers.Mapou
November 20, 2015
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J-Mac, your comment @250 is the perfect example of why the layman cannot talk about or understand abiogenesis. Thank you for that, I had a good laugh.Alicia Cartelli
November 20, 2015
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"Right, but you can’t get that initial ribozyme without an intelligent designer." False. Ribozyme is a strand of nucleic acid folded in on itself. As demonstrated above ,the early earth was capable of synthesizing nucleic acids and folding is a spontaneous process. The only requirement is the correct sequence to form an active site. Production of enough random nucleic acid sequences, in my opinion, will eventually produce a strand with catalytic activity. In the way that many of the amino acids of a protein can be swapped out while still retaining function, The nucleotides of these early ribozymes do not need to be perfectly conserved during molecular evolution and a number of variants can all produce a catalytic molecule. It is a small subset of the nucleotides that are the most important in this molecule.Alicia Cartelli
November 20, 2015
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Alicia ignores Spiegelman's Monster, an experiment that supports nature's tendency towards the more simple. Alicia:
Recent studies have shown that, starting with a ribozyme capable of joining two ribonucleotides together, random mutations and copying produces ribozymes capable of replication activity.
Right, but you can't get that initial ribozyme without an intelligent designer. Perhaps someone needs to take Alicia's proposal and put it to the test. Take all of the synthesized RNAs, ribozymes and amino acids you need, Alicia, put them into a lipid membrane vesicle and see what happens. Eric gave you all of that in the OP. Merely saying that you have what Eric gave you does not mean those ingredients can produce the product. BTW you still need to address the shopping cart issue- meaning the different biomolecules arise in different environments and you need to bring them together.Virgil Cain
November 20, 2015
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Eric Anderson #242: (...) natural selection has nothing to do with producing new biological structures, systems, organisms, and so on. Nor does it have anything to do with the production of the information [note: not Shannon information] required for those biological systems. Natural selection is irrelevant to the task and the problem at hand. Yes, we all agree that some creatures can die off and reduce the available variety that was already in the population. Big deal. It doesn’t tell us one useful thing about how the biological innovation was produced.
Species selection does not account for the origin of the different anatomical traits that distinguish one species from another. Species selection, as conceived by the proponents of punctuated equilibrium, acts on species and traits that already exist. Indeed, when Stanley, Gould, and Eldredge envisioned natural selection acting to favor the most fit species over another in a competition for survival, they presupposed the existence of a pool of different species and, therefore, also the existence of some mechanism for producing the traits that characterize those different species. That mechanism, however, would necessarily need to generate those differentiating traits before species could enter into competition with each other. Species selection eliminates less fit species in a competition for survival; it does not generate the traits that distinguish species and establish the basis for interspecies competition. [Stephen Meyer, ch.7, Darwin's Doubt]
Box
November 20, 2015
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Here’s a very brief overview of the basic supporting work done on abiogenesis
Can you provide a reference link? Have you ever done this internet thing before? Andrewasauber
November 20, 2015
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Do you know nothing about science or do you just love the word “IF?”
You're the one who keeps using it. I'll stop when you do. Andrewasauber
November 20, 2015
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J-Mac- The initial energy came from hydrothermal vents, alkaline vents- not the black smokers- that produced cell-like pores in the rocks that formed along the ridge. Allegedly that is what got the Krebs cycle going and forming ATP synthase was a breeze after that-> Nick Lane "Life Ascending" chapter 1 (2009) Allegedly that is the best they had 6 years ago.Virgil Cain
November 20, 2015
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Here's a very brief overview of the basic supporting work done on abiogenesis and I have taken it a step further for EA at the end and talk briefly about a simplified example of the evolution of the first living organism. Enjoy. Miller-Urey demonstrated that methane, ammonia, and hydrogen gases in a highly favorable early earth model could produce cyanide, formaldehyde, and amino acids. Subsequent studies demonstrated similar results in more realistic models. Amino acids are repeatedly produced by early earth models and have also been found in meteorites. Mimicking volcanic gases flowing through rock crevices produces amino acids and in fact, it tends to produce some of the natural amino acids over the other, unnatural residues. UV light in early earth models produce aldehydes, which are still important intermediates in amino acid synthesis. Polymerization of amino acids, although unfavorable, can be driven by certain conditions. Simply through energy input in the presence of minerals, researchers have demonstrated the formation of protein polymers. We have also observed amino acid polymerization at hydrothermal vents. Amino acids in cooler water have been shown to polymerize when carbon and sulfur-containing gases (commonly ejected by hydrothermal vents) are also present. Important reactants have been hypothesized to accumulate on layers of mineral deposits in the early earth environment; dissolved gases are attracted to these minerals which helps to concentrate them to drive chemical reactions. The minerals function as catalysts as they are reactive in solution and their importance can still be seen at the active site of many enzymes today. The production of acetic acid from dissolved carbon dioxide and hydrogen is spontaneous and still used today by bacteria. Acetic acid is also an important intermediate in the pathway that produces acetyl-CoA, a molecule still used by all living organisms. Recent research has shown that a variety of larger organic molecules can be produced by early earth models, including those important to the eventual synthesis of nucleotides. Free radical production is much more likely in the early earth atmosphere, where there is no ozone layer. Free radicals are highly reactive and computer models have demonstrated the formation of formaldehyde through these types of reactions. In the presence of heat or UV radiation, formaldehyde molecules are able to link together, forming more complicated organic molecules such as sugars. Both 5- and 6-carbon sugars are produced in these models and other studies have shown that enrichment of the 5-carbon sugars occurs on minerals outside of hydrothermal vents. 3-carbon ketoses and other molecules related to sugars have also been found in meteorites. Hydrogen cyanide was also likely produced in the early earth atmosphere as shown in Miller-Urey, and it is an important precursor for nucleic base production. Early earth atmospheric models eventually led to the production of all five nucleic bases. Prebiotic simulations have demonstrated activation of nucleotides through addition of phosphate groups, and further studies have shown that these nucleotides can polymerize in the presence of minerals. Even without nucleotide activation, polymerization of nucleic acids over 90 bases long has been demonstrated to occur when both heat and small lipids are included. Recent studies have shown that, starting with a ribozyme capable of joining two ribonucleotides together, random mutations and copying produces ribozymes capable of replication activity. This enzyme is now capable of using itself as a template, to copy fragments of itself. Other studies have demonstrated molecular evolution by starting with random pools of nucleic acids and selection of nucleic acids that connect uracil base to ribose sugar. After 11 rounds of selection, the ribozyme population was 1,000,000x better at catalyzing the reaction in comparison to the uncatalyzed reaction. Numerous other studies have produced ribozymes with a host of different catalytic activities. Simple lipids have been produced through early earth model systems using hydrogen, carbon dioxide and mineral catalysts. Lipids with amphipathic properties have also been discovered in meteorites. These molecules form simple membrane structures spontaneously due to the hydrophobic effect and provide an environment more suitable for life inside the first protocells. These early cell membranes provide the ability to concentrate reactants and protect products of chemical reactions. Membrane permeability of small molecules can be altered by simple proteins that span the hydrophobic layer and also by temperature changes. Simple vesicles can join together, in essence “growing” and vibrations of the surrounding media can cause them to replicate. Ions and ribonucleotides are known to diffuse through fatty acid membranes and the formation of these membranes is facilitated by minerals as well. It is hypothesized that the first replicating molecule did not consist of RNA, but instead was made up of simpler nucleic acids, which consisted of simpler nucleotide molecules. Nucleic acid-polypeptide hybrid molecules have been proposed, in which nucleic bases are connected by peptide bonds instead of phosphodiester bonds. These simpler molecules are capable of both catalytic activity and acting as a template; and their ability to direct synthesis of RNA as we know it today has been demonstrated, as they have similar 3D geometries. This would allow for evolution from a pre-RNA world to an RNA world. The catalytic repertoire of ribozymes seen in nature today is quite small, however synthetic ribozymes have demonstrated a wide variety of reactions, even rivaling proteins. The distinction between proteinaceous enzymes and ribozymes seems to be the efficiency with which they catalyze reactions, not the range of possible reactions. The ability of ribozymes to catalyze their own replication has been demonstrated, but only in fragments. Ribozymes able to ligate short nucleotide strands, which has already been demonstrated, would piece these fragments together, producing more replicating ribozymes. The efficiency of this ligation reaction would be increased by containing the replicating ribozyme and nucleic acid fragments within a membrane consisting of fatty acids or some derivative of these amphipathic molecules. This would be the first living cell. Sealing these ribozymes into protocells allows for evolution of these first organisms based on not just structure of subcellular components, but also how these components interact with each other. Replication of these protocells would be driven by physical agitation, unevenly splitting the intracellular components into new protocells and providing more variation for selection to act on. Experiments have demonstrated that selection from pools of random RNA molecules can produce RNA polymers that bind tightly to amino acids. These RNA molecules tend to have sequences identical to the codons still used by today’s translational system. This shows the potential for a limited genetic code, of which the remnants cans still be seen today. Synthetic ribozymes have been shown to catalyze tRNA charging, moving the early translational system closer to the more efficient system seen today. Evolution of this early translational system would make protein synthesis more efficient and eventually lead to a protein-dominated world.Alicia Cartelli
November 20, 2015
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Alicia Cartelli, Please give as at least one example how this issue with the origins of life was experimentally resolve: Enzymes are needed to produce ATP. But energy from ATP is needed to produce enzymes. However, DNA is required to make enzymes, but enzymes are required to make DNA. However, proteins can be made only by a cell, but a cell can be made only with specific proteins. So, how have those obvious issues been resolved by the experiments YOU CLAIM to be in abundance? Please provide specific experiments. I can't waitJ-Mac
November 20, 2015
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They are IF statements because they are contingent on the experimental results. Do you know nothing about science or do you just love the word "IF?"Alicia Cartelli
November 20, 2015
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